FileFormat

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Specifies the format of the input file.

For most NGS modules, this includes the following:

FASTQ
FASTA
QSEQ -- an Illumina format
AUTO -- automatically detect format based on file type

The long read aligner also allows for:
SFF


For importing already mapped reads:

BAM - BAM format (http://samtools.sourceforge.net/SAM1.pdf)

SAM - SAM format (http://samtools.sourceforge.net/SAM1.pdf)